DAISIE_loglik_CS: Computes the loglikelihood of the DAISIE model with...

In xieshu95/Test-Trasie: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Description

Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given colonization and branching times for lineages on an island, and a set of model parameters. The output is a loglikelihood value

Usage

DAISIE_loglik_CS(pars1, pars2, datalist, methode = "lsodes",
  CS_version = 1, abstolint = 1e-16, reltolint = 1e-10)

Arguments

pars1	Contains the model parameters: pars1[1] corresponds to lambda^c (cladogenesis rate) pars1[2] corresponds to mu (extinction rate) pars1[3] corresponds to K (clade-level carrying capacity) pars1[4] corresponds to gamma (immigration rate) pars1[5] corresponds to lambda^a (anagenesis rate) pars1[6] corresponds to lambda^c (cladogenesis rate) for an optional subset of the species pars1[7] corresponds to mu (extinction rate) for an optional subset of the species pars1[8] corresponds to K (clade-level carrying capacity) for an optional subset of the species pars1[9] corresponds to gamma (immigration rate) for an optional subset of the species pars1[10] corresponds to lambda^a (anagenesis rate) for an optional subset of the species pars1[11] corresponds to p_f (fraction of mainland species that belongs to the second subset of species The elements 6:10 and 11 are optional, that is,pars1 should either contain 5, 10 or 11 elements. If 10, then the fraction of potential colonists of type 2 is computed from the data. If 11, then pars1[11] is used, overruling any information in the data.
pars2	Contains the model settings pars2[1] corresponds to lx = length of ODE variable x pars2[2] corresponds to ddmodel = diversity-dependent model, model of diversity-dependence, which can be one of ddmodel = 0 : no diversity dependence ddmodel = 1 : linear dependence in speciation rate ddmodel = 11: linear dependence in speciation rate and in immigration rate ddmodel = 2 : exponential dependence in speciation rate ddmodel = 21: exponential dependence in speciation rate and in immigration rate pars2[3] corresponds to cond = setting of conditioning cond = 0 : conditioning on island age cond = 1 : conditioning on island age and non-extinction of the island biota pars2[4] sets whether parameters and likelihood should be printed (1) or not (0)
datalist	Data object containing information on colonisation and branching times. This object can be generated using the DAISIE_dataprep function, which converts a user-specified data table into a data object, but the object can of course also be entered directly. It is an R list object with the following elements. The first element of the list has two or three components: $island_age - the island age Then, depending on whether a distinction between types is made, we have: $not_present - the number of mainland lineages that are not present on the island or: $not_present_type1 - the number of mainland lineages of type 1 that are not present on the island $not_present_type2 - the number of mainland lineages of type 2 that are not present on the island The remaining elements of the list each contains information on a single colonist lineage on the island and has 5 components: $colonist_name - the name of the species or clade that colonized the island $branching_times - island age and stem age of the population/species in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic species. For cladogenetic species these should be island age and branching times of the radiation including the stem age of the radiation. $stac - the status of the colonist * Non_endemic_MaxAge: 1 * Endemic: 2 * Endemic&Non_Endemic: 3 * Non_Endemic: 4 * Endemic_Singleton_MaxAge: 5 * Endemic_Clade_MaxAge: 6 * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number of island species that were not sampled for particular clade (only applicable for endemic clades) $type1or2 - whether the colonist belongs to type 1 or type 2
methode	Method of the ODE-solver. See package deSolve for details. Default is "lsodes"
CS_version	For internal testing purposes only. Default is 1, the original DAISIE code.
abstolint	Absolute tolerance of the integration
reltolint	Relative tolerance of the integration

Value

The loglikelihood

Author(s)

Rampal S. Etienne & Bart Haegeman

References

Valente, L.M., A.B. Phillimore and R.S. Etienne (2015). Equilibrium and non-equilibrium dynamics simultaneously operate in the Galapagos islands. Ecology Letters 18: 844-852.

See Also

DAISIE_ML, DAISIE_sim

Examples

utils::data(Galapagos_datalist_2types)
pars1 = c(0.195442017,0.087959583,Inf,0.002247364,0.873605049,
          3755.202241,8.909285094,14.99999923,0.002247364,0.873605049,0.163)
pars2 = c(100,11,0,1)
DAISIE_loglik_all(pars1,pars2,Galapagos_datalist_2types)

xieshu95/Test-Trasie documentation built on Dec. 18, 2019, 7:34 a.m.